QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2

Literature Information

Publication Date 2013-01-17
DOI 10.1039/C3CP44181D
Impact Factor 3.676
Authors

Kai Welke, Hiroshi C. Watanabe, Tino Wolter, Marcus Elstner


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Abstract

Channelrhodopsin-2 is a light-gated ion channel, which has been studied intensively over the last decade. Vibrational spectroscopic experiments started to shed light on the structural changes, that occur during the photocycle, especially in the hydrogen-bonded network surrounding the protonated D156 and C128 – the DC gate. However, the interpretation of these experiments was only based on homology models. Since then, an X-ray structure and better computational models became available. In this article, we show that in combination with a recent reparametrization, the approximate DFT method, DFTB, is able to describe the effects of hydrogen bonding on the CO stretch vibration in carboxylic acids reliably and agrees well with full DFT results. We apply DFTB in a QM/MM framework to perform vibrational analysis of buried aspartic acids in bacteriorhodopsin and channelrhodopsin-2. Using this approach, we can simulate the FTIR spectral difference between D115 in the dark-adapted and K states of bacteriorhodopsin. The FTIR experiments on the DC gate in channelrhodopsin-2 are well described using an indirect model, where D156 and C128 are bridged via a water molecule.

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
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Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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